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rrwick / Unicycler

hybrid assembly pipeline for bacterial genomes
GNU General Public License v3.0
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errors during spades Assembling no outputs #12

Closed giampe79 closed 7 years ago

giampe79 commented 7 years ago

Dear Unicycler author, I have tried Unicycler tool to assemble my genome (2,5 milion base) with a set of paired Illumina reads and a set of PacBio reads, I have used the docker container to run it. The run of command failed , I;m reporting below the relative message, Could you help me to fix these errors? COMMAND LAUNCHED: c1780c8c[unicycler_input_result]# unicycler -1 RAMS001_dd_S28_L004_R1_001.fastq -2 RAMS001_dd_S28_L004_R2_001.fastq -l R125-G01.1-Reads.fastq -o ./output_dirUnicycler --pilon_path=/usr/local/share/pilon-1.20-0/pilon-1.20.jar

REPORT Starting Unicycler Command: /usr/local/bin/unicycler -1 RAMS001_dd_S28_L004_R1_001.fastq -2 RAMS001_dd_S28_L004_R2_001.fastq -l R125-G01.1-Reads.fastq -o ./output_dirUnicycler --pilon_path=/usr/local/share/pilon-1.20-0/pilon-1.20.jar

Making output directory: /home/unicycler_input_result/output_dirUnicycler

SPAdes read error correction Command: /usr/local/bin/spades.py -1 /home/unicycler_input_result/RAMS001_dd_S28_L004_R1_001.fastq -2 /home/unicycler_input_result/RAMS001_dd_S28_L004_R2_001.fastq -o /home/unicycler_input_result/output_dirUnicycler/spades_assembly_temp/read_correction --threads 8 --only-error-correction

Corrected reads: /home/unicycler_input_result/output_dirUnicycler/spades_assembly_temp/corrected_1.fastq.gz /home/unicycler_input_result/output_dirUnicycler/spades_assembly_temp/corrected_2.fastq.gz /home/unicycler_input_result/output_dirUnicycler/spades_assembly_temp/corrected_u.fastq.gz

Choosing k-mer range for assembly Median read length: 151 K-mer range: 27, 47, 63, 77, 89, 99, 107, 115, 121, 127

Conducting SPAdes assemblies K-mer Segments Dead ends Score 27 too complex 47 too complex 63 325 0 3.08e-03 77 260 0 3.85e-03 89 178 0 5.62e-03 99 157 0 6.37e-03 107 139 0 7.19e-03 115 124 0 8.06e-03 121 115 0 8.70e-03 Traceback (most recent call last): File "/usr/local/bin/unicycler", line 11, in load_entry_point('unicycler==0.2.0', 'console_scripts', 'unicycler')() File "/usr/local/lib/python3.5/site-packages/unicycler/unicycler.py", line 79, in main args.expected_linear_seqs) File "/usr/local/lib/python3.5/site-packages/unicycler/spades_func.py", line 152, in get_best_spades_graph row_extra_text={best_kmer_row: ' \u2190 best'}) File "/usr/local/lib/python3.5/site-packages/unicycler/misc.py", line 628, in print_table print(indenter + row_str, flush=True) UnicodeEncodeError: 'ascii' codec can't encode character '\u2190' in position 48: ordinal not in range(128) c1780c8c[unicycler_input_result]#

thanks in advance Annalisa

rrwick commented 7 years ago

Hi Annalisa,

I'm happy to report that this bug has been fixed! https://github.com/rrwick/Unicycler/commit/c97159770522fb42fc749998350a81698870f273

The first (and simplest) solution would be to just run a more recent version of Unicycler through Docker:

docker run quay.io/biocontainers/unicycler:0.3.0b--py35_0 unicycler

I've updated the Unicycler README to show this one instead of the previous version (0.2.0) which still has the bug. However, this version isn't completely up-to-date. I've submitted an updated recipe to BioConda for the new version I just made (v0.3.0), but I must confess that I'm not very savvy with this Bioconda/BioContainers stuff.

Alternatively, you could clone and install Unicycler yourself, without Docker. This will let you get the most recent version, but you'll have to make sure you have all the other dependencies installed, like SPAdes.

Ryan